Zarr: Optimize region="auto" detection
#8997
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dcherian
commented
May 3, 2024
| for k, v in self.get_variables().items() | ||
| if k in existing_variable_names | ||
| }, | ||
| {k: self.open_store_variable(name=k) for k in existing_variable_names}, |
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Just open the needed variables instead of opening all of them.
dcherian
commented
May 3, 2024
Comment on lines
+807
to
+812
| variable = conventions.decode_cf_variable( | ||
| dim, self.open_store_variable(dim).compute() | ||
| ) | ||
| assert variable.dims == (dim,) | ||
| index = pd.Index(variable.data) | ||
| idxs = index.get_indexer(ds[dim].data) |
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Lines 812-817: This is the main logic change.
dcherian
commented
May 3, 2024
xarray/backends/zarr.py
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| region[dim] = slice(idxs[0], idxs[-1] + 1) | ||
| return region | ||
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| def _validate_and_autodetect_region(self, ds, region) -> dict[str, slice]: |
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directly copied over
dcherian
commented
May 3, 2024
| write_empty=write_empty_chunks, | ||
| ) | ||
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| if region is not None: |
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Moved down so we only open the Zarr store once.
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dcherian
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May 3, 2024
| ds = xr.Dataset({"foo": ("x", np.arange(30))}, coords={"x": np.arange(30)}) | ||
| # Any of the following region specifications are valid | ||
| ds.isel(x=slice(0, 10)).to_zarr(path, region="auto") | ||
| ds.isel(x=slice(10, 20)).to_zarr(path, region={"x": "auto"}) |
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This last line does not do what it looks like it's doing if there are no indexes!
dcherian
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region="auto" detection
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Looks great! |
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Thanks for taking a look, Max! |
andersy005
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May 10, 2024
* Zarr: Optimize region detection * Fix for unindexed dimensions. * Better example * small cleanup
andersy005
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May 10, 2024
* main: Avoid auto creation of indexes in concat (#8872) Fix benchmark CI (#9013) Avoid extra read from disk when creating Pandas Index. (#8893) Add a benchmark to monitor performance for large dataset indexing (#9012) Zarr: Optimize `region="auto"` detection (#8997) Trigger CI only if code files are modified. (#9006) Fix for ruff 0.4.3 (#9007) Port negative frequency fix for `pandas.date_range` to `cftime_range` (#8999) Bump codecov/codecov-action from 4.3.0 to 4.3.1 in the actions group (#9004) Speed up localize (#8536) Simplify fast path (#9001) Add argument check_dims to assert_allclose to allow transposed inputs (#5733) (#8991) Fix syntax error in test related to cupy (#9000)
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* backend-indexing: Trigger CI only if code files are modified. (pydata#9006) Enable explicit use of key tuples (instead of *Indexer objects) in indexing adapters and explicitly indexed arrays (pydata#8870) add `.oindex` and `.vindex` to `BackendArray` (pydata#8885) temporary enable CI triggers on feature branch Avoid auto creation of indexes in concat (pydata#8872) Fix benchmark CI (pydata#9013) Avoid extra read from disk when creating Pandas Index. (pydata#8893) Add a benchmark to monitor performance for large dataset indexing (pydata#9012) Zarr: Optimize `region="auto"` detection (pydata#8997) Trigger CI only if code files are modified. (pydata#9006) Fix for ruff 0.4.3 (pydata#9007) Port negative frequency fix for `pandas.date_range` to `cftime_range` (pydata#8999) Bump codecov/codecov-action from 4.3.0 to 4.3.1 in the actions group (pydata#9004) Speed up localize (pydata#8536) Simplify fast path (pydata#9001) Add argument check_dims to assert_allclose to allow transposed inputs (pydata#5733) (pydata#8991) Fix syntax error in test related to cupy (pydata#9000)
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ZarrStoreso we only open the store once.pd.Indexdirectly to "auto"-infer the region.The diff is large mostly because a bunch of code moved from
backends/api.pytobackends/zarr.py